7FDB | pdb_00007fdb

CryoEM Structures of Reconstituted V-ATPase,State2

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

CryoEM Structures of Reconstituted V-ATPase and Oxr1-bound V1 Reveal a Novel Mechanism of Regulation.

Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens, S., Roh, S.H.

(2021) EMBO J 


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Yeast Vacuolar ATPase A subunit
A, C, E
617Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
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UniProt GroupP17255
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit B
B, D, F
517Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P16140 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit E
G, I, K
233Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit G
H, J, L
122Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit D256Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit F118Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit C392Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA5
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT)469Saccharomyces cerevisiae S288C, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
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Find proteins for Q9UI12 (Homo sapiens)
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PHAROS:  Q9UI12
GTEx:  ENSG00000047249 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Yeast Vacuolar ATPase a subunit840Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit dR [auth S]345Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit c''S [auth T]213Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit c'T [auth U]164Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit c160Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit eCA [auth d]73Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
V0 assembly protein 1DA [auth e]265Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Yeast Vacuolar ATPase f subunitEA [auth f]85Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C5R9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP0C5R9
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM058600
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA228340
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM141908

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Data collection